Molluscs assemblages inhabiting subtidal habitats (sandy bottoms, photophilic and sciaphilic hard bottoms, Posidonia oceanica seagrass beds) represent a valuable part of coastal biodiversity and were studied in four Italian Marine Protected Areas. Quantitative samplings were carried out in late spring -summer of 2015. A total of 776 individuals were identified, belonging to the classes of Polyplacophora (5 species, 24 individuals), Gastropoda (62 sp., 240 ind.), Bivalvia (51 sp., 488 ind.), and Scaphopoda (3 sp., 24 ind.). Multivariate analyses revealed significant inter-habitat differences in the composition of mollusc assemblages, especially between soft bottom and all the other habitats. In all MPAs, the highest species richness and feeding guilds occurred in the photophilic hard bottom, where, in contrast, a lower number of individuals was found. On the contrary, in the soft bottom the highest number of individuals and the lower species richness and feeding guilds were found. Although the results pointed out some intrahabitat differences among MPAs, the molluscan assemblages showed a valuable degree of taxonomic and trophic similarity, especially in vegetated habitats. These results are of primary importance for ecosystem functioning and management as the considered habitats are the most relevant of the coastal zones.